How would Athena expect Medusa to have avoided being raped, and by a deity no less?
Does Poseidon warrant no blame in the eyes of the ancient Greeks? What about in Athena's eyes?
Is it being raped in her temple that angers Athena, or is it simply having intercourse there (ie. would consensual sex between Medusa and Poseidon have warranted punishment)?
How was the myth of Medusa's rape and subsequent punishment viewed by the Romans? Did they also agree that Medusa was to blame?
I assume the answer lies somewhere in Greek notions of sexuality and gender roles, but it seems like a grave injustice, like punishing someone for falling down a flight of stairs or for getting wet in a rainstorm (ie. for circumstances beyond your control). Any insight would be appreciated!
It's not even a Greek story! The only source for this variant of the Medusa story is Ovid's Metamorphoses, 4.790-803. No source other than Ovid gives any hint that she ever underwent any change: she was Gorgo all along, both dangerous and beautiful, and always had been.
There are two Greek accounts that touch on the subject of her liaison with Poseidon, and her offence to Athena. In the Hesiodic Theogony, 277-9, Poseidon has sex with her in a flowery meadow; there's no indication of rape (though that interpretation is not ruled out), and no punishment for the act. In pseudo-Apollodoros, Library 2.4.3, we're told that "some say" Athena commissioned Perseus to kill Medusa because she had dared to compare her beauty to that of Athena.
So the variant that you've found is a specific Roman poet's idiosyncratic innovation on the story. Your question comes down to a literary interpretation of Ovid, and why he introduced the idea of Medusa being changed from a beautiful maiden into a horrible monster. The most obvious answer to that would be that he was looking for a way of reconciling two contrasting ways in which the Gorgons were depicted: sometimes they were depicted as dreadful monsters, sometimes as beautiful maidens. It's not hard to imagine other answers that would also make sense; none of them can be rigorously excluded.
Edit. Victoria Rimell's 2006 book Ovid's Lovers: Desire, Difference, and the Poetic Imagination goes into considerable depth about the deeper meaning of Ovid's Medusa story from the perspective of Lacanian psychoanalysis. (That doesn't necessarily mean her book is meaningless mumbo-jumbo: Lacan can be a route into tracing Ovid's creative processes, whether or not you believe he has a valid scientific model of human psychology.) She doesn't touch on the subject of punishment per se, but goes into the nature of the erotic gaze which, by objectifying, effectively turns the object of desire into "stone": she's kind of a mirror image of Pygmalion, whose erotic attention creates the object of his desire rather than desiring a real person. Both objectify, but in opposite ways. Medusa's erotic power ends up being subverted by a literal mirror wielded by Perseus: in effect he punishes her for having agency. Now, none of this has anything to do with the inner meaning of myths, but I find it an attractive literary exegesis of Ovid. But literature is a matter of taste.